Dear Vincenzo,
For ML estimates the edge length are the expected number of substitutions per
site, which depends on the product of rate and time. So you need either a rate
estimate or calibration points to estimate the time. If you divide the edge
length by the rate the edges should be proportio
__
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>
--
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Senior Scientist
Institute of Molecular Biotechnology
TU Graz
https://www
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> > R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
> [[alternative HTML version deleted]]
>
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-phylo mailing list - R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-pr
taxon? I've noticed adding a 'mrca'
> argument also increases computation time and if I am reinventing the wheel
> it would be nice to know if I am overthinking things.
>
> Sincerely,
> Russell
>
> [[alternative HTML version deleted]]
>
> ______
tp://www.mail-archive.com/r-sig-phylo@r-project.org/
>
--
Klaus Schliep
Senior Scientist
Institute of Computational Biotechnology
TU Graz
https://icbt.tugraz.at
https://www.phangorn.org/ <http://www.phangorn.org/>
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> >
> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&
Hi Sebastian,
there is an implementation of the SH-test and SOWH-test in phangorn. Send
me an mail off list if you have problems using them.
Regards,
Klaus
On Jun 8, 2018 8:50 AM, "Sebastian Y. Müller" wrote:
Dear all,
I'd was wondering how to best perform a test to determine test
disagreement
1, Cidade Universitária,
> São Paulo - SP, CEP: 05508-090, Brasil.
>
> [[alternative HTML version deleted]]
>
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(R 3.4.1)
>>> parallel 3.4.1 2017-06-30 local
>>> prettyunits 1.0.2 2015-07-13 CRAN (R 3.4.1)
>>> progress 1.1.2 2016-12-14 CRAN (R 3.4.1)
>>> R62.2.2 2017-06-17 CRAN (R 3.4.0)
>>> Rcpp 0.12.12 2017-07-15
g list - R-sig-phylo@r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > > Searchable archive at http://www.mail-archive.com/r-
> > > sig-ph...@r-project.org/
> > >
> >
> > [[alternative HTML version deleted]]
> >
> >
> >
> >
turn(NULL)
>>>Ntip <- length(phy$tip.label)
>>>rootnd <- Ntip + 1L
>>>
>>>pars <- integer(phy$Nnode) # worst case assignment, usually far too
>>> long
>>>mrcaind <- 1L # index in pars of the mrca node. will return highest
>>&
> >>> <https://www.avast.com/sig-email?utm_medium=email&utm_
> source=link&utm_campaign=sig-email&utm_content=emailclient>
> >>>
> >>>
> >>>
> >>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >>>
&g
tnd);
> }
> idx <- which(pars == cpar);
> if (idx > mrcaind) {
> mrcaind <- idx;
> }
> done <- TRUE;
> } else {
> # keep going!
> cnd
mated way to do it.
> > >> :-)
> > >> Sincerely,
> > >> V.
> --
> Vojtěch Zeisek
> https://trapa.cz/en/
>
> Department of Botany, Faculty of Science
> Charles University, Prague, Czech Republic
> https://www.natur.cuni.cz/biology/botany/
>
> Institute
ttp://www.mail-archive.com/r-
>> sig-ph...@r-project.org/
>>
>>
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> Searchable archive at http://www.mail-ar
rzbin...@dkfz-heidelberg.de> wrote:
> Dear Klaus,
>
>
>
> Thanks a lot for your help
>
>
>
> and what is in that case xx and yy?
>
>
>
> Justyna
>
>
>
> *From:* Klaus Schliep [mailto:klaus.schl...@gmail.com]
> *Sent:* Friday, February 24, 2017 6:13 PM
Josef Puchta
>>
>> VAT-ID No.: DE143293537
>>
>>
>>
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rtment of Genome Sciences and Department of Biology,
> University of Washington, Box 355065, Seattle, WA 98195-5065 USA
>
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> sig-ph...@r-project.org/
>
--
Klaus Schliep
Postdoctoral Fellow
Revell La
mailing list - R-sig-phylo@r-project.org
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> sig-ph...@r-project.org/
>
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/
ncouver, Canada
>
> [[alternative HTML version deleted]]
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> sig-ph...@r-project.org/
>
I had a look at the tree. There seems a bug in extract.clades, when the
tree was rooted before with the root() function. extract.clade() seem to
expect some ordering of nodes which seems not satisfied (and it looks as it
was written a long time ago).
I just wrote a small function (easier than to d
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> sig-ph...@r-project.org/
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-ph...@r-project.org/
>
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/
[[alternative HTML version delete
g
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-ph...@r-project.org/
>
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/
[[alternative HTML versio
>><https://stat.ethz.ch/mailman/listinfo/r-sig-phylo>
> >>>><https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> >><https://stat.ethz.ch/mailman/listinfo/r-sig-phylo>>
> >>>>> Searchable archive at
> >&g
Dear Rav,
write.dna() from ape just does this.
Klaus
On Sep 12, 2016 9:07 AM, "Bhuller, Ravneet" <
ravneet.bhulle...@imperial.ac.uk> wrote:
> Hi Thibaut,
>
> Is there anyway I can save the concatenated alignment (created using apex
> and the concatenate function) in FASTA format?
>
> Regards,
>
>
>
> option = 1 => using the criterion you suggested below
> option = 2 => using the current 'variance' criterion
>
> And other criteria could be added.
>
> What do you think?
>
> Best,
>
> Emmanuel
>
>
> Le 17/08/2016 à 19:16, Klaus Schliep a
ultrametric(phy, tol = .Machine$double.eps^0.5).
> According to ?.Machine this value does not depend on the machine precision.
> On my laptop, it gives:
>
> R> .Machine$double.eps^0.5
> [1] 1.490116e-08
>
> Best,
>
> Emmanuel
>
>
> Le 16/08/2016 à 18:15,
tionary Biology
> Room 2071, Kraus Natural Sciences Building
> Ann Arbor MI 48109-1079
> josep...@umich.edu
>
>
>
> On 16 Aug, 2016, at 10:15, Klaus Schliep wrote:
>
> Hello all,
> this may come be surprising to many, but consulting the manual
> ?is.ultrametric can be
Hello all,
this may come be surprising to many, but consulting the manual
?is.ultrametric can be helpful. Why not simply try e.g.
is.ultrametric(tree, tol=.01)
So in this sense RTFM
Regards,
Klaus
On Aug 16, 2016 9:31 AM, "Martin Dohrmann"
wrote:
>
> Am 16.08.2016 um 15:20 schrieb Joseph W.
f the workshop, course leaders Drs. April Wright
and Klaus Schliep (with Dr. Liam Revell participating remotely) will
provide an introduction to the primary data structures and methods of
common phylogenetic R packages, the basics of computational algorithms
for phylogenies, and an overview of pa
HI Kamilla,
can you send me your code and data and what phangorn version are you using?
Cheers,
Klaus
On Tue, Jun 14, 2016 at 6:42 PM, Kamila Naxerova
wrote:
> Hi all,
>
> I am trying to attach bootstrap values to a small tree (just 4 taxa).
> plotBS() in the phangorn package gives me the follow
> > R-sig-phylo mailing list - R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > Searchable archive at
> > http://www.mail-archive.com/r-sig-phylo@r-project.org/
> >
>
> [[alternative HTML version deleted
t; PhD candidate
>
> Wageningen University
> Laboratory of Biochemistry
> Dreijenlaan 3
> 6703 HA Wageningen
> The Netherlands
>
> Phone 31 317483387
> e-mail: gudrun.gy...@wur.nl
>
> - - - - - - - - - - - - - - - - - -
>
> Project information:
> http://www.wagening
; G
>
>
>
> Gudrun Gygli, MSc
>
> PhD candidate
>
> Wageningen University
> Laboratory of Biochemistry
> Dreijenlaan 3
> 6703 HA Wageningen
> The Netherlands
>
> Phone 31 317483387
> e-mail: gudrun.gy...@wur.nl
>
> - - - - - - - - - - - - - - - - -
710
> Cell 423-676-7489
> Office/lab 423-439-4359
> Fax423-439-5958
>
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> http://www.
Hi all,
you have to install the Biostrings package from bioconductor. Than it
should works. Phangorn has a dependency on biostrings and phytools depend
on phangorn.
Have a nice weekend
Klaus
Am 09.01.2016 16:35 schrieb "Donald Miles" :
> Dear All,
>
> I receive the same error as Gabriela when I tr
s,foo)
> Error in lapply(ttrees, foo) : object 'ttrees' not found
> > class(trees)<-"multiPhylo"
> > fit.equal<-t(mapply(fit.model,trees,xy))
> Error in mapply(fit.model, trees, xy) : object 'xy' not found
> > mean(fit.equal[,1]) ## should
Dear Tim,
I added an optional argument sitewise to the CI and RI function in
phangorn. The vector may contains NaN if the function is undefined: pscore
of 0 for CI, uninformative site for RI.
It is now on github:
library(devtools)
install_github("KlausVigo/phangorn")
Cheers,
Klaus
On Thu, Dec 1
lled any bioconductor packages, chances are that you also
installed Biostrings package are pretty high.
Regards,
Klaus
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
[[alternative HTML version deleted]]
__
http://www.linkedin.com/in/anandksrao>
> _
> CTTATTGTTGAACTTOAATGGTGCTAATGATCCTCGTOTCTCCTGAACGT - translate THAT!
>
> [[alternative HTML version deleted]]
>
> ________
That's fine with me.
On Tue, Oct 20, 2015 at 3:29 PM, David Bapst wrote:
> Ah, thanks, Klaus! I was is it alright with you if I merge these edits
> into paleotree?
> -Dave
>
> On Tue, Oct 20, 2015 at 1:15 PM, Klaus Schliep
> wrote:
> > Hi Gustavo & Davi
Best,
>
> *Gustavo Burin Ferreira, **Msc.*
> Instituto de Biociências
> Universidade de São Paulo
> Tel: (11) 98525-8948
>
> On Tue, Oct 20, 2015 at 5:15 PM, Klaus Schliep
> wrote:
>
>> Hi Gustavo & David,
>>
>> I attached a file that contains a
t; > > Searchable archive at
> > > http://www.mail-archive.com/r-sig-phylo@r-project.org/
> > >
> > >
> > >
> > > --
> > > David W. Bapst, PhD
> > > Adjunct Asst. Professor, Geology and Geol. Eng.
> > > South Dakota Schoo
1.0135
> > write.tree(phy=ltr, file="")
> [1]
>
> "((t2:0.06701971429,t1:0.06701971429):2.686176768,(t5:1.207768321,(t6:0.4984853178,(t4:1.013489985,t3:1.013489985):0.09146602338):0.1028123128):1.545428161);"
> >
> > tr_wFossils = read.tree(file=""
~--~--~---
>
> [[alternative HTML version deleted]]
>
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Dear Kamila,
plotBS checks if trees are rooted or not and if not midpoint roots the tree
nrooted <- root(nj(dist),outgroup=x)
is.rooted(nrooted) # returns FALSE
however the ape function does not pick up that the tree is rooted.
Add the argument resolve.root=TRUE:
nrooted <- root(nj(dist),outgroup=
leX = FALSE, col = 1, width = 1, cex = 0.8)
>
>
> (THIS DOES NOT WORK!)
>
>
> Thanks in advance for helping me with this!
>
>
> Marina
>
> [[alternative HTML version deleted]]
>
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>
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>
--
Klaus
.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
[[alternative HTML version deleted]]
__
t;
> http://webpages.sdsmt.edu/~dbapst/
> http://cran.r-project.org/web/packages/paleotree/index.html
>
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>
ng that something like pml (phangorn) can be modified to do
> that, but I haven't been able to figure it out myself yet.
>
> Thanks in advance,
> George
>
> [[alternative HTML version deleted]]
>
> _______
> R-sig-phylo m
using phytools on a PC. Anybody
> know what gives here?
>
> cheers,
>
> Gabe
>
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> sig-ph...@r-project.org/
>
--
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Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
[[alternative HTML vers
Hello Manabu,
try Ancestors from phangorn.
Regards
Klaus
Am 04.11.2014 08:12 schrieb "Manabu Sakamoto" :
> Dear list,
>
> I was wondering if there was an existing function to identify all the nodes
> (e.g., phylo$edge[,1]) along a pathway from the root to any given tip.
>
> I've found Descendants
Hello Vojt�ch,
have you looked into consensusNet in phangorn?
Regards,
Klaus
Am 03.11.2014 03:10 schrieb "Vojt�ch Zeisek" :
> Hello,
> let's say I have many gene trees (all have same labels) in one multiPhylo
> object. The trees are not fully congruent. One of the reasons can be
> hybridization
gt; [1] 2 1 1
>
> There are four positions (X1-X4) but only three site patterns and
> therefore three parsimony scores.
>
> Thank you.
>
> Rob
>
>
>
>
>
> [[alternative HTML version deleted]]
>
> ___
> R-sig-phyl
absence of the trait, and ideally is capable
>> of generating a dataframe of the appropriate format for the above functions
>> automatically. It seems that a function to do this should exist already,
>> but as I can't seem to find anything I would appreciate some help
>>
gt; />/ Thanks,
> />/
> />/ Robin
> />/
> />/ Robin van Velzen
> />/ PhD student
> />/ Biosystematics Group
> />/ Wageningen University
> />/
> />/ Wageningen Campus, Radix building 107, Room W4.Aa.095
> />/ Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
&
"S28"
> >> "S18" "S5""S11" "S18.1" "S20.1" "S16.1"
> >
> >> When I plot any tree in treeP, S18.1, S20.1 and S16.1 appear together
> with
> >> S18, S20 and S16, as intended. So why are t
correct tree and the OutbreakTools function
> >> is not. We can see the why with last three lines in the console:
> >>
> >> identical(tree1$tip.label,tree2$tip.label)
> >>
> >> [1] TRUE
> >>
> >> identical(tree1$edge.length,tree2$edge.length)
&g
392:195)),(A393:198,(A394:269,(A395:97,A396:184)
>
> )),((A397:18,(A398:281,(A399:343,(A400:238,A401:280,(A402:163,(A403:308,
>
> ((A404:399,(A405:317,(A406:40,A407:191))),(((A408:230,A409:350),(A410:112,(A
>
> 411:346,(A412:68,(A413:387,(A414:332,A415:333)),(A416:250,(A417:232,(A41
>
> 8:348,(A419:67,(
ystématique et Evolution Case postale 39
> UMR CNRS 7205
>
> 57 rue cuvier
>
> FRANCE-75005 Paris
>
> portable +33629375132
> poste 0140793200
>
> [[alternative HTML version deleted]]
>
>
> ___
> R-sig-ph
-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
--
Klaus Schliep
[[alternative HTML version deleted]]
___
R-sig-phylo mailing l
ls=sort(unique(char)))
>
> anc<-ancestral.pars(tree,char,type="MPR") #here's the crash!
>
>
>
> --
> David W. Bapst, PhD
> Adjunct Asst. Professor, Geology and Geol. Eng.
> South Dakota School of Mines and Te
this is the problem?
> Should I convert it?
>
> Thanks!
>
> ------
> *De:* Klaus Schliep
> *Para:* Fabricia Nascimento
> *Cc:* "r-sig-phylo@r-project.org"
> *Enviadas:* Terça-feira, 8 de Abril de 2014 13:20
>
> *Assunto:* Re: [R-sig-ph
>
> Thanks!
> Fabricia.
>
> ----------
> *De:* Klaus Schliep
> *Para:* Fabricia Nascimento
> *Cc:* "r-sig-phylo@r-project.org"
> *Enviadas:* Terça-feira, 8 de Abril de 2014 13:13
> *Assunto:* Re: [R-sig-phylo] chronos and gammaStat
>
> Hello Frabricia,
&
gt;
>
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>
--
Klaus Schliep
[[alter
lor="black",
> edge.width=3,add=T)
>
> --
> Grato
> Augusto C. A. Ribas
>
> Site Pessoal: http://recologia.com.br/ <http://augustoribas.heliohost.org>
> Github: https://github.com/Squiercg
> Lattes: http://lattes.cnpq.br/7355685961127056
>
> [[alter
his how to predict the number of possible trees?
>
> Best Wishes, Augusto Ribas
>
> --
> Grato
> Augusto C. A. Ribas
>
> Site Pessoal: http://recologia.com.br/ <http://augustoribas.heliohost.org>
> Github: https://github.com/Squiercg
> Lattes: http://lattes.c
ctive and
>> has two levels of menus.
>>
>> Joe
>>
>> Joe Felsenstein j...@gs.washington.edu
>> Department of Genome Sciences and Department of Biology,
>> University of Washington, Box 355065, Seattle, WA 98195-5065 USA
>>
>
> ___
or ways I could modify the pglmm.fit function to
> speed the estimation process?
>
> Thanks in advance for any suggestions. And thanks to Tony and Matt for
> developing these models and making them available in R.
>
> Dan
>
> ______
;
> Thank you & cheers,
> Sereina
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
--
Klaus
-- Forwarded message --
From: Klaus Schliep
Date: Thu, Aug 22, 2013 at 6:12 PM
Subject: Re: [R-sig-phylo] Collapsing branches with low bootstrap values
To: "Naxerova, Kamila"
Hi Kamila,
try function pruneTree in phangorn.
data(woodmouse)
f <- function(x) nj(di
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--
Klaus Schliep
Phylogenomics Lab at the University of V
!
>
> Douda
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>
tinfo/r-sig-phylo
> Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
--
Klaus Schliep
Phylogenomics Lab at the University of Vigo, Spain
http://darwin.uvigo.es/kschliep/
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rong!
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> Any input welcome,
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> cheers,
> Xavier
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Klaus S
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ltiPhylo"
plot(tr2)
for(i in 1:1000){print(i);write.tree(tr2[[i]])} # may helps find you
the trees which fail
write.tree(tr2, file="result.tre")
Cheers,
Klaus
On 2/28/13, Klaus Schliep wrote:
> Dear John,
>
> can you please be a bit more specific with your error message.
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Klaus Schliep
Phylogenomics Lab at the University of Vigo, Spain
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[1] -2.220446e-16
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> I am posting this in case it is of interest to others. As a quick fix,
> I am now rounding x.
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> Thanks,
> Kelly
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Hi Alastair
here is a solution, probably not the most elegant. You may look into
the function as.splits,
phangorn:::print.splits to improve the output and lento for a nicer
way of plotting your results.
x <- y <- list()
for (i in 1:100) {x[[i]] <- rtree(20); y[[i]] <- rtree(20)}
z = c(x,y)
z = l
Hi Alastair,
I discovered two problems with the analysis. One is your data, which
contains too many transitions and so you lost most of the information
about your the process which generated the data.
There is also a problem with prop.clades, which does not take care
enough for different orderings
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Klaus Schliep
Université Paris 6 (Pierre et Marie Curie)
9, Quai Saint-Bernard, 75005 Paris
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Hello Ben,
is your tree ultrametric? Do you have a e.g. UPGMA tree? This would
explain your observation. You can test your tree with
is.ultrametric(trx).
Regards,
Klaus
On 5/27/12, Ben Weinstein wrote:
> Hi all,
>
> I'm trying to decide if this an R error, or an error in
> how I've implement
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Université Paris 6 (Pierre et Marie Curie)
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Hello John,
it seems the chronogram contains the heights instead of the
edge.lengths for each edge.
Here is a small function to convert the tree. You should check if it
is the same as in treefinder.
convert.tree <- function(tree){
el = numeric(max(tree$edge))
el[tree$edge[,2]] = tree$edge.l
;
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Hi Brian,
I just uploaded a new version of phangorn on CRAN (1.6-0) which solved
the plotBS issue. The new version also returns silently a tree with
the bootstrap values as node labels. So if you want to export a tree
with edge length and bootstrap values, you should do something like
this:
treeR
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